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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        About MultiQC

        This report was generated using MultiQC, version 1.33

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        MultiQC is developed by Seqera.

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        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-12-10, 21:45 UTC based on data in: /scratch4/workspace/julia_mcdonough_student_uml_edu-novogene_dwnld/fastqc
        Because this report contains a lot of samples, you may need to click 'Show plot' to see some graphs.

        General Statistics

        Showing 240/240 rows and 3/6 columns.
        Sample NameDupsGCAvg lenMedian lenFailedSeqs
        B1_B1_O01_gi_1_val_1
        58.7%
        42.0%
        149bp
        150bp
        18%
        35.5M
        B1_B1_O01_gi_2_val_2
        58.4%
        42.0%
        149bp
        150bp
        18%
        35.5M
        B1_Nu_O03_gi_1_val_1
        65.2%
        42.0%
        149bp
        150bp
        18%
        50.2M
        B1_Nu_O03_gi_2_val_2
        64.8%
        42.0%
        149bp
        150bp
        27%
        50.2M
        B1_W5_O50_gi_1_val_1
        59.5%
        42.0%
        149bp
        150bp
        18%
        33.9M
        B1_W5_O50_gi_2_val_2
        59.3%
        43.0%
        149bp
        150bp
        18%
        33.9M
        B2_B5_O51_gi_1_val_1
        62.2%
        42.0%
        149bp
        150bp
        18%
        38.0M
        B2_B5_O51_gi_2_val_2
        61.8%
        42.0%
        149bp
        150bp
        18%
        38.0M
        B2_C4_O40_gi_1_val_1
        61.6%
        42.0%
        149bp
        150bp
        18%
        38.6M
        B2_C4_O40_gi_2_val_2
        61.3%
        42.0%
        149bp
        150bp
        18%
        38.6M
        B2_Nu_O12_gi_1_val_1
        70.8%
        43.0%
        149bp
        150bp
        18%
        51.2M
        B2_Nu_O12_gi_2_val_2
        70.5%
        43.0%
        149bp
        150bp
        27%
        51.2M
        B3_B4_O41_gi_1_val_1
        62.0%
        42.0%
        149bp
        150bp
        18%
        31.9M
        B3_B4_O41_gi_2_val_2
        61.6%
        42.0%
        149bp
        150bp
        18%
        31.9M
        B3_C3_O30_gi_1_val_1
        68.9%
        43.0%
        149bp
        150bp
        18%
        34.9M
        B3_C3_O30_gi_2_val_2
        68.5%
        43.0%
        149bp
        150bp
        18%
        34.9M
        B3_C6_O66_gi_1_val_1
        66.0%
        42.0%
        149bp
        150bp
        18%
        52.3M
        B3_C6_O66_gi_2_val_2
        65.7%
        42.0%
        149bp
        150bp
        27%
        52.3M
        B3_H4_O41_gi_1_val_1
        88.2%
        42.0%
        149bp
        150bp
        18%
        33.5M
        B3_H4_O41_gi_2_val_2
        87.8%
        42.0%
        149bp
        150bp
        18%
        33.5M
        B3_Nu_O24_gi_1_val_1
        96.6%
        49.0%
        149bp
        150bp
        27%
        2.3M
        B3_Nu_O24_gi_2_val_2
        95.9%
        49.0%
        149bp
        150bp
        27%
        2.3M
        B3_W1_O06_gi_1_val_1
        62.5%
        42.0%
        149bp
        150bp
        18%
        36.1M
        B3_W1_O06_gi_2_val_2
        62.3%
        42.0%
        149bp
        150bp
        18%
        36.1M
        B3_W4_O41_gi_1_val_1
        60.2%
        42.0%
        149bp
        150bp
        18%
        33.4M
        B3_W4_O41_gi_2_val_2
        59.7%
        43.0%
        149bp
        150bp
        18%
        33.4M
        B4_B2_O19_gi_1_val_1
        63.0%
        42.0%
        149bp
        150bp
        18%
        35.5M
        B4_B2_O19_gi_2_val_2
        62.7%
        42.0%
        149bp
        150bp
        18%
        35.5M
        B4_B3_O32_gi_1_val_1
        63.5%
        43.0%
        149bp
        150bp
        18%
        36.2M
        B4_B3_O32_gi_2_val_2
        63.2%
        43.0%
        149bp
        150bp
        18%
        36.2M
        B4_C5_O56_gi_1_val_1
        65.1%
        43.0%
        149bp
        150bp
        18%
        36.6M
        B4_C5_O56_gi_2_val_2
        64.7%
        43.0%
        149bp
        150bp
        27%
        36.6M
        B4_H1_O07_gi_1_val_1
        78.7%
        44.0%
        149bp
        150bp
        18%
        30.1M
        B4_H1_O07_gi_2_val_2
        78.3%
        44.0%
        149bp
        150bp
        18%
        30.1M
        B4_H5_O55_gi_1_val_1
        68.7%
        43.0%
        149bp
        150bp
        27%
        31.2M
        B4_H5_O55_gi_2_val_2
        68.1%
        43.0%
        149bp
        150bp
        27%
        31.2M
        B4_Nu_O32_gi_1_val_1
        67.1%
        43.0%
        149bp
        150bp
        18%
        54.5M
        B4_Nu_O32_gi_2_val_2
        66.8%
        43.0%
        149bp
        150bp
        27%
        54.5M
        B4_W2_O19_gi_1_val_1
        59.1%
        42.0%
        149bp
        150bp
        18%
        32.7M
        B4_W2_O19_gi_2_val_2
        58.7%
        42.0%
        149bp
        150bp
        18%
        32.7M
        B4_W6_O67_gi_1_val_1
        67.0%
        42.0%
        149bp
        150bp
        18%
        36.5M
        B4_W6_O67_gi_2_val_2
        66.9%
        42.0%
        149bp
        150bp
        18%
        36.5M
        B5_B6_O69_gi_1_val_1
        65.8%
        42.0%
        149bp
        150bp
        18%
        44.6M
        B5_B6_O69_gi_2_val_2
        65.4%
        42.0%
        149bp
        150bp
        27%
        44.6M
        B5_C1_O09_gi_1_val_1
        68.2%
        44.0%
        149bp
        150bp
        18%
        38.6M
        B5_C1_O09_gi_2_val_2
        67.8%
        44.0%
        149bp
        150bp
        18%
        38.6M
        B5_H2_O21_gi_1_val_1
        62.8%
        42.0%
        149bp
        150bp
        18%
        38.8M
        B5_H2_O21_gi_2_val_2
        62.6%
        42.0%
        149bp
        150bp
        18%
        38.8M
        B5_Nu_O36_gi_1_val_1
        59.4%
        42.0%
        149bp
        150bp
        18%
        40.3M
        B5_Nu_O36_gi_2_val_2
        59.0%
        42.0%
        149bp
        150bp
        27%
        40.3M
        B5_W3_O33_gi_1_val_1
        59.1%
        42.0%
        149bp
        150bp
        18%
        36.2M
        B5_W3_O33_gi_2_val_2
        58.8%
        42.0%
        149bp
        150bp
        18%
        36.2M
        B6_C2_O24_gi_1_val_1
        59.1%
        42.0%
        149bp
        150bp
        18%
        34.6M
        B6_C2_O24_gi_2_val_2
        58.9%
        42.0%
        149bp
        150bp
        18%
        34.6M
        B6_H3_O35_gi_1_val_1
        64.3%
        42.0%
        149bp
        150bp
        18%
        46.8M
        B6_H3_O35_gi_2_val_2
        64.0%
        42.0%
        149bp
        150bp
        27%
        46.8M
        B6_H6_O72_gi_1_val_1
        56.7%
        42.0%
        149bp
        150bp
        18%
        31.3M
        B6_H6_O72_gi_2_val_2
        56.6%
        42.0%
        149bp
        150bp
        18%
        31.3M
        B6_Nu_O47_gi_1_val_1
        59.6%
        42.0%
        149bp
        150bp
        18%
        42.0M
        B6_Nu_O47_gi_2_val_2
        59.3%
        42.0%
        149bp
        150bp
        27%
        42.0M
        C1_C4_W37_gi_1_val_1
        67.9%
        44.0%
        149bp
        150bp
        18%
        37.0M
        C1_C4_W37_gi_2_val_2
        67.5%
        44.0%
        149bp
        150bp
        18%
        37.0M
        C1_H2_W13_gi_1_val_1
        67.2%
        42.0%
        149bp
        150bp
        18%
        56.0M
        C1_H2_W13_gi_2_val_2
        67.0%
        42.0%
        149bp
        150bp
        18%
        56.0M
        C1_H6_W62_gi_1_val_1
        63.7%
        42.0%
        149bp
        150bp
        18%
        32.6M
        C1_H6_W62_gi_2_val_2
        63.3%
        42.0%
        149bp
        150bp
        18%
        32.6M
        C1_Nu_W01_gi_1_val_1
        62.0%
        42.0%
        149bp
        150bp
        18%
        47.7M
        C1_Nu_W01_gi_2_val_2
        61.8%
        42.0%
        149bp
        150bp
        27%
        47.7M
        C1_Nu_W05_gi_1_val_1
        63.5%
        42.0%
        149bp
        150bp
        18%
        41.6M
        C1_Nu_W05_gi_2_val_2
        63.2%
        42.0%
        149bp
        150bp
        27%
        41.6M
        C2_B2_W16_gi_1_val_1
        63.1%
        42.0%
        149bp
        150bp
        18%
        32.6M
        C2_B2_W16_gi_2_val_2
        62.7%
        42.0%
        149bp
        150bp
        18%
        32.6M
        C2_C1_W03_gi_1_val_1
        61.6%
        42.0%
        149bp
        150bp
        18%
        34.3M
        C2_C1_W03_gi_2_val_2
        61.3%
        42.0%
        149bp
        150bp
        18%
        34.3M
        C2_H1_W04_gi_1_val_1
        62.3%
        42.0%
        149bp
        150bp
        18%
        32.4M
        C2_H1_W04_gi_2_val_2
        61.9%
        42.0%
        149bp
        150bp
        18%
        32.4M
        C2_Nu_W15_gi_1_val_1
        64.2%
        42.0%
        149bp
        150bp
        18%
        44.7M
        C2_Nu_W15_gi_2_val_2
        63.8%
        42.0%
        149bp
        150bp
        27%
        44.7M
        C2_W2_W15_gi_1_val_1
        67.0%
        43.0%
        149bp
        150bp
        18%
        37.9M
        C2_W2_W15_gi_2_val_2
        66.6%
        43.0%
        149bp
        150bp
        18%
        37.9M
        C3_B3_W30_gi_1_val_1
        61.9%
        43.0%
        149bp
        150bp
        18%
        33.1M
        C3_B3_W30_gi_2_val_2
        61.6%
        43.0%
        149bp
        150bp
        18%
        33.1M
        C3_C2_W17_gi_1_val_1
        66.2%
        42.0%
        149bp
        150bp
        18%
        37.1M
        C3_C2_W17_gi_2_val_2
        65.7%
        42.0%
        149bp
        150bp
        18%
        37.1M
        C3_Nu_W21_gi_1_val_1
        65.6%
        42.0%
        149bp
        150bp
        18%
        55.2M
        C3_Nu_W21_gi_2_val_2
        65.4%
        42.0%
        149bp
        150bp
        27%
        55.2M
        C3_W3_W29_gi_1_val_1
        63.3%
        43.0%
        149bp
        150bp
        18%
        34.0M
        C3_W3_W29_gi_2_val_2
        62.9%
        43.0%
        149bp
        150bp
        18%
        34.0M
        C4_B1_W07_gi_1_val_1
        58.9%
        42.0%
        149bp
        150bp
        18%
        34.0M
        C4_B1_W07_gi_2_val_2
        58.7%
        42.0%
        149bp
        150bp
        18%
        34.0M
        C4_B5_W56_gi_1_val_1
        73.1%
        42.0%
        149bp
        150bp
        18%
        48.9M
        C4_B5_W56_gi_2_val_2
        72.7%
        42.0%
        149bp
        150bp
        27%
        48.9M
        C4_C6_W67_gi_1_val_1
        62.0%
        42.0%
        149bp
        150bp
        18%
        44.8M
        C4_C6_W67_gi_2_val_2
        61.8%
        42.0%
        149bp
        150bp
        27%
        44.8M
        C4_H5_W56_gi_1_val_1
        56.8%
        42.0%
        149bp
        150bp
        18%
        31.1M
        C4_H5_W56_gi_2_val_2
        56.6%
        42.0%
        149bp
        150bp
        18%
        31.1M
        C4_Nu_W29_gi_1_val_1
        64.2%
        42.0%
        149bp
        150bp
        18%
        58.4M
        C4_Nu_W29_gi_2_val_2
        63.7%
        42.0%
        149bp
        150bp
        27%
        58.4M
        C5_B4_W46_gi_1_val_1
        64.1%
        42.0%
        149bp
        150bp
        18%
        35.3M
        C5_B4_W46_gi_2_val_2
        63.8%
        43.0%
        149bp
        150bp
        18%
        35.3M
        C5_C3_W33_gi_1_val_1
        66.5%
        42.0%
        149bp
        150bp
        18%
        41.4M
        C5_C3_W33_gi_2_val_2
        65.9%
        42.0%
        149bp
        150bp
        27%
        41.4M
        C5_W1_W09_gi_1_val_1
        63.8%
        42.0%
        149bp
        150bp
        18%
        33.9M
        C5_W1_W09_gi_2_val_2
        63.5%
        42.0%
        149bp
        150bp
        18%
        33.9M
        C5_W4_W45_gi_1_val_1
        64.1%
        43.0%
        149bp
        150bp
        18%
        33.4M
        C5_W4_W45_gi_2_val_2
        63.7%
        43.0%
        149bp
        150bp
        18%
        33.4M
        C6_B6_W71_gi_1_val_1
        64.2%
        43.0%
        149bp
        150bp
        18%
        38.5M
        C6_B6_W71_gi_2_val_2
        63.8%
        43.0%
        149bp
        150bp
        18%
        38.5M
        C6_C5_W59_gi_1_val_1
        62.6%
        42.0%
        149bp
        150bp
        18%
        40.8M
        C6_C5_W59_gi_2_val_2
        62.2%
        42.0%
        149bp
        150bp
        27%
        40.8M
        C6_H3_W36_gi_1_val_1
        60.5%
        42.0%
        149bp
        150bp
        18%
        42.3M
        C6_H3_W36_gi_2_val_2
        60.1%
        42.0%
        149bp
        150bp
        27%
        42.3M
        C6_H4_W48_gi_1_val_1
        58.2%
        42.0%
        149bp
        150bp
        18%
        35.5M
        C6_H4_W48_gi_2_val_2
        58.0%
        42.0%
        149bp
        150bp
        18%
        35.5M
        C6_Nu_W42_gi_1_val_1
        69.6%
        42.0%
        149bp
        150bp
        18%
        42.1M
        C6_Nu_W42_gi_2_val_2
        69.3%
        42.0%
        149bp
        150bp
        27%
        42.1M
        C6_W6_W72_gi_1_val_1
        60.2%
        42.0%
        149bp
        150bp
        18%
        34.3M
        C6_W6_W72_gi_2_val_2
        59.9%
        42.0%
        149bp
        150bp
        18%
        34.3M
        C_W5_W52_gi_1_val_1
        64.7%
        42.0%
        149bp
        150bp
        18%
        37.0M
        C_W5_W52_gi_2_val_2
        64.3%
        42.0%
        149bp
        150bp
        18%
        37.0M
        H1_B2_B13_gi_1_val_1
        60.9%
        42.0%
        149bp
        150bp
        18%
        31.2M
        H1_B2_B13_gi_2_val_2
        60.7%
        42.0%
        149bp
        150bp
        18%
        31.2M
        H1_B6_B61_gi_1_val_1
        59.6%
        42.0%
        149bp
        150bp
        18%
        34.9M
        H1_B6_B61_gi_2_val_2
        59.3%
        42.0%
        149bp
        150bp
        18%
        34.9M
        H1_C6_B62_gi_1_val_1
        66.5%
        42.0%
        149bp
        150bp
        18%
        51.2M
        H1_C6_B62_gi_2_val_2
        66.2%
        42.0%
        149bp
        150bp
        27%
        51.2M
        H1_Nu_B08_gi_1_val_1
        63.0%
        42.0%
        149bp
        150bp
        18%
        42.4M
        H1_Nu_B08_gi_2_val_2
        62.8%
        42.0%
        149bp
        150bp
        27%
        42.4M
        H1_W4_B38_gi_1_val_1
        65.3%
        42.0%
        149bp
        150bp
        18%
        36.2M
        H1_W4_B38_gi_2_val_2
        64.9%
        42.0%
        149bp
        150bp
        18%
        36.2M
        H1_W5_B49_gi_1_val_1
        87.6%
        42.0%
        149bp
        150bp
        18%
        33.1M
        H1_W5_B49_gi_2_val_2
        87.1%
        42.0%
        149bp
        150bp
        18%
        33.1M
        H2_B5_B51_gi_1_val_1
        65.8%
        42.0%
        149bp
        150bp
        18%
        34.9M
        H2_B5_B51_gi_2_val_2
        65.6%
        42.0%
        149bp
        150bp
        27%
        34.9M
        H2_C1_B04_gi_1_val_1
        62.3%
        42.0%
        149bp
        150bp
        18%
        35.9M
        H2_C1_B04_gi_2_val_2
        62.0%
        42.0%
        149bp
        150bp
        18%
        35.9M
        H2_H1_B03_gi_1_val_1
        63.2%
        42.0%
        149bp
        150bp
        18%
        35.9M
        H2_H1_B03_gi_2_val_2
        62.9%
        42.0%
        149bp
        150bp
        18%
        35.9M
        H2_H5_B51_gi_1_val_1
        66.5%
        44.0%
        149bp
        150bp
        18%
        39.4M
        H2_H5_B51_gi_2_val_2
        66.4%
        44.0%
        149bp
        150bp
        18%
        39.4M
        H2_Nu_B14_gi_1_val_1
        66.9%
        43.0%
        149bp
        150bp
        18%
        54.6M
        H2_Nu_B14_gi_2_val_2
        66.5%
        43.0%
        149bp
        150bp
        27%
        54.6M
        H2_W2_B16_gi_1_val_1
        60.8%
        42.0%
        149bp
        150bp
        18%
        34.5M
        H2_W2_B16_gi_2_val_2
        60.7%
        42.0%
        149bp
        150bp
        18%
        34.5M
        H3_B4_B41_gi_1_val_1
        77.2%
        42.0%
        149bp
        150bp
        27%
        35.7M
        H3_B4_B41_gi_2_val_2
        76.9%
        42.0%
        149bp
        150bp
        27%
        35.7M
        H3_C5_B54_gi_1_val_1
        65.5%
        42.0%
        149bp
        150bp
        18%
        40.1M
        H3_C5_B54_gi_2_val_2
        65.3%
        42.0%
        149bp
        150bp
        27%
        40.1M
        H3_H4_B41_gi_1_val_1
        85.3%
        43.0%
        149bp
        150bp
        18%
        31.7M
        H3_H4_B41_gi_2_val_2
        84.9%
        43.0%
        149bp
        150bp
        18%
        31.7M
        H3_H6_B66_gi_1_val_1
        61.1%
        42.0%
        149bp
        150bp
        18%
        34.7M
        H3_H6_B66_gi_2_val_2
        60.8%
        42.0%
        149bp
        150bp
        27%
        34.7M
        H3_Nu_B18_gi_1_val_1
        68.1%
        42.0%
        149bp
        150bp
        18%
        39.6M
        H3_Nu_B18_gi_2_val_2
        67.6%
        42.0%
        149bp
        150bp
        36%
        39.6M
        H3_W3_B30_gi_1_val_1
        59.0%
        42.0%
        149bp
        150bp
        18%
        32.7M
        H3_W3_B30_gi_2_val_2
        58.6%
        42.0%
        149bp
        150bp
        18%
        32.7M
        H3_W6_B66_gi_1_val_1
        61.8%
        42.0%
        149bp
        150bp
        18%
        30.1M
        H3_W6_B66_gi_2_val_2
        61.5%
        42.0%
        149bp
        150bp
        18%
        30.1M
        H4_H2_B19_gi_1_val_1
        64.2%
        42.0%
        149bp
        150bp
        18%
        39.8M
        H4_H2_B19_gi_2_val_2
        64.0%
        42.0%
        149bp
        150bp
        18%
        39.8M
        H4_Nu_B28_gi_1_val_1
        61.3%
        42.0%
        149bp
        150bp
        18%
        45.1M
        H4_Nu_B28_gi_2_val_2
        60.8%
        42.0%
        149bp
        150bp
        27%
        45.1M
        H4_W1_B07_gi_1_val_1
        56.6%
        42.0%
        149bp
        150bp
        18%
        32.0M
        H4_W1_B07_gi_2_val_2
        56.3%
        42.0%
        149bp
        150bp
        18%
        32.0M
        H5_B1_B09_gi_1_val_1
        60.7%
        42.0%
        149bp
        150bp
        18%
        35.2M
        H5_B1_B09_gi_2_val_2
        60.5%
        42.0%
        149bp
        150bp
        18%
        35.2M
        H5_B3_B34_gi_1_val_1
        61.2%
        42.0%
        149bp
        150bp
        18%
        35.7M
        H5_B3_B34_gi_2_val_2
        60.9%
        42.0%
        149bp
        150bp
        18%
        35.7M
        H5_C2_B22_gi_1_val_1
        62.4%
        42.0%
        149bp
        150bp
        18%
        31.2M
        H5_C2_B22_gi_2_val_2
        62.1%
        43.0%
        149bp
        150bp
        18%
        31.2M
        H5_C4_B46_gi_1_val_1
        59.4%
        42.0%
        149bp
        150bp
        18%
        31.4M
        H5_C4_B46_gi_2_val_2
        59.1%
        42.0%
        149bp
        150bp
        18%
        31.4M
        H5_Nu_B35_gi_1_val_1
        58.5%
        41.0%
        149bp
        150bp
        18%
        39.5M
        H5_Nu_B35_gi_2_val_2
        58.0%
        41.0%
        149bp
        150bp
        27%
        39.5M
        H6_C3_B36_gi_1_val_1
        64.7%
        42.0%
        149bp
        150bp
        18%
        34.7M
        H6_C3_B36_gi_2_val_2
        64.3%
        42.0%
        149bp
        150bp
        18%
        34.7M
        H6_H3_B35_gi_1_val_1
        64.9%
        42.0%
        149bp
        150bp
        18%
        49.3M
        H6_H3_B35_gi_2_val_2
        64.6%
        42.0%
        149bp
        150bp
        27%
        49.3M
        H6_Nu_B45_gi_1_val_1
        66.1%
        43.0%
        149bp
        150bp
        18%
        40.3M
        H6_Nu_B45_gi_2_val_2
        65.7%
        43.0%
        149bp
        150bp
        27%
        40.3M
        W1_C1_G02_gi_1_val_1
        61.4%
        42.0%
        149bp
        150bp
        18%
        35.3M
        W1_C1_G02_gi_2_val_2
        61.1%
        42.0%
        149bp
        150bp
        18%
        35.3M
        W1_C6_G61_gi_1_val_1
        70.3%
        42.0%
        149bp
        150bp
        18%
        55.1M
        W1_C6_G61_gi_2_val_2
        70.0%
        42.0%
        149bp
        150bp
        27%
        55.1M
        W1_H5_G49_gi_1_val_1
        66.4%
        42.0%
        149bp
        150bp
        18%
        54.9M
        W1_H5_G49_gi_2_val_2
        66.4%
        42.0%
        149bp
        150bp
        18%
        54.9M
        W1_Nu_G02_gi_1_val_1
        58.5%
        42.0%
        149bp
        150bp
        18%
        54.8M
        W1_Nu_G02_gi_2_val_2
        58.2%
        42.0%
        149bp
        150bp
        27%
        54.8M
        W1_W1_G01_gi_1_val_1
        65.0%
        42.0%
        149bp
        150bp
        18%
        37.0M
        W1_W1_G01_gi_2_val_2
        64.7%
        42.0%
        149bp
        150bp
        18%
        37.0M
        W1_W6_G62_gi_1_val_1
        64.4%
        42.0%
        149bp
        150bp
        18%
        49.7M
        W1_W6_G62_gi_2_val_2
        64.3%
        42.0%
        149bp
        150bp
        27%
        49.7M
        W2_B2_G04_gi_1_val_1
        68.9%
        43.0%
        149bp
        150bp
        18%
        31.4M
        W2_B2_G04_gi_2_val_2
        68.6%
        43.0%
        149bp
        150bp
        18%
        31.4M
        W2_B6_G64_gi_1_val_1
        59.8%
        42.0%
        149bp
        150bp
        18%
        32.5M
        W2_B6_G64_gi_2_val_2
        59.6%
        42.0%
        149bp
        150bp
        18%
        32.5M
        W2_C2_G15_gi_1_val_1
        67.0%
        43.0%
        149bp
        150bp
        18%
        36.5M
        W2_C2_G15_gi_2_val_2
        66.6%
        43.0%
        149bp
        150bp
        18%
        36.5M
        W2_Nu_G15_gi_1_val_1
        62.4%
        42.0%
        149bp
        150bp
        18%
        39.2M
        W2_Nu_G15_gi_2_val_2
        62.2%
        42.0%
        149bp
        150bp
        27%
        39.2M
        W3_B5_G54_gi_1_val_1
        64.4%
        42.0%
        149bp
        150bp
        18%
        41.0M
        W3_B5_G54_gi_2_val_2
        64.1%
        42.0%
        149bp
        150bp
        27%
        41.0M
        W3_C3_G29_gi_1_val_1
        63.3%
        42.0%
        149bp
        150bp
        18%
        32.7M
        W3_C3_G29_gi_2_val_2
        62.9%
        42.0%
        149bp
        150bp
        18%
        32.7M
        W3_H2_G18_gi_1_val_1
        61.2%
        42.0%
        149bp
        150bp
        18%
        33.6M
        W3_H2_G18_gi_2_val_2
        60.9%
        42.0%
        149bp
        150bp
        18%
        33.6M
        W3_H3_G30_gi_1_val_1
        64.1%
        43.0%
        149bp
        150bp
        18%
        49.1M
        W3_H3_G30_gi_2_val_2
        63.6%
        43.0%
        149bp
        150bp
        27%
        49.1M
        W3_Nu_G21_gi_1_val_1
        71.1%
        43.0%
        149bp
        150bp
        18%
        53.1M
        W3_Nu_G21_gi_2_val_2
        70.7%
        43.0%
        149bp
        150bp
        27%
        53.1M
        W4_C5_G55_gi_1_val_1
        64.5%
        43.0%
        149bp
        150bp
        18%
        36.2M
        W4_C5_G55_gi_2_val_2
        64.4%
        43.0%
        149bp
        150bp
        27%
        36.2M
        W4_H1_G08_gi_1_val_1
        58.4%
        42.0%
        149bp
        150bp
        18%
        35.8M
        W4_H1_G08_gi_2_val_2
        58.1%
        42.0%
        149bp
        150bp
        18%
        35.8M
        W4_Nu_G27_gi_1_val_1
        62.7%
        42.0%
        149bp
        150bp
        18%
        47.3M
        W4_Nu_G27_gi_2_val_2
        62.3%
        42.0%
        149bp
        150bp
        27%
        47.3M
        W4_W5_G56_gi_1_val_1
        65.8%
        43.0%
        149bp
        150bp
        27%
        35.8M
        W4_W5_G56_gi_2_val_2
        65.5%
        43.0%
        149bp
        150bp
        27%
        35.8M
        W5_B2_G21_gi_1_val_1
        64.1%
        42.0%
        149bp
        150bp
        18%
        41.4M
        W5_B2_G21_gi_2_val_2
        63.8%
        42.0%
        149bp
        150bp
        27%
        41.4M
        W5_C4_G45_gi_1_val_1
        64.2%
        42.0%
        149bp
        150bp
        18%
        30.9M
        W5_C4_G45_gi_2_val_2
        63.7%
        42.0%
        149bp
        150bp
        18%
        30.9M
        W5_H4_G46_gi_1_val_1
        62.5%
        42.0%
        149bp
        150bp
        18%
        34.7M
        W5_H4_G46_gi_2_val_2
        62.4%
        42.0%
        149bp
        150bp
        18%
        34.7M
        W5_W2_G22_gi_1_val_1
        57.8%
        42.0%
        149bp
        150bp
        18%
        35.6M
        W5_W2_G22_gi_2_val_2
        57.5%
        42.0%
        149bp
        150bp
        18%
        35.6M
        W6_B3_G35_gi_1_val_1
        60.2%
        42.0%
        149bp
        150bp
        18%
        33.2M
        W6_B3_G35_gi_2_val_2
        60.0%
        42.0%
        149bp
        150bp
        18%
        33.2M
        W6_B4_G48_gi_1_val_1
        65.2%
        43.0%
        149bp
        150bp
        18%
        34.8M
        W6_B4_G48_gi_2_val_2
        64.9%
        43.0%
        149bp
        150bp
        18%
        34.8M
        W6_H6_G71_gi_1_val_1
        64.0%
        42.0%
        149bp
        150bp
        18%
        33.2M
        W6_H6_G71_gi_2_val_2
        63.7%
        42.0%
        149bp
        150bp
        18%
        33.2M
        W6_Nu_G41_gi_1_val_1
        65.4%
        42.0%
        149bp
        150bp
        18%
        44.1M
        W6_Nu_G41_gi_2_val_2
        65.1%
        42.0%
        149bp
        150bp
        27%
        44.1M
        W6_Nu_G45_gi_1_val_1
        59.4%
        42.0%
        149bp
        150bp
        18%
        34.3M
        W6_Nu_G45_gi_2_val_2
        59.0%
        42.0%
        149bp
        150bp
        27%
        34.3M
        W6_W3_G36_gi_1_val_1
        63.9%
        43.0%
        149bp
        150bp
        18%
        33.5M
        W6_W3_G36_gi_2_val_2
        63.7%
        43.0%
        149bp
        150bp
        18%
        33.5M
        W6_W4_G48_gi_1_val_1
        66.4%
        42.0%
        149bp
        150bp
        18%
        34.2M
        W6_W4_G48_gi_2_val_2
        66.1%
        43.0%
        149bp
        150bp
        18%
        34.2M
        Expand table

        FastQC

        Version: 0.12.1

        Quality control tool for high throughput sequencing data.http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms
        240

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores
        240

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        $ Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content
        220
        11
        9

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content
        240

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution
        240

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels
        240

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        GAAGTTGTTAAGTAGCGGTTCTTAAACTTTTAGGTGGTTGAGTATAGGAG
        237
        21796081
        0.2364%
        GTTGTTAAGTAGCGGTTCTTAAACTTTTAGGTGGTTGAGTATAGGAGTAT
        236
        15220007
        0.1651%
        GCCCGATTTTGCGTATCACATCCTTAAAGAAATTAGTTCGAGAATTTACT
        159
        9224890
        0.1000%
        AGAAGTTGTTAAGTAGCGGTTCTTAAACTTTTAGGTGGTTGAGTATAGGA
        141
        8414249
        0.0913%
        CCCGATTTTGCGTATCACATCCTTAAAGAAATTAGTTCGAGAATTTACTG
        144
        7737522
        0.0839%
        GTTGAGTATAGGAGTATTAGAAAGCCCATAATCTAGCTATATTAAGTCTG
        58
        2837547
        0.0308%
        ATTCAACTTTATCTAAAGGAACTCGGCAAATACTAAGCCTCGCCTGTTTA
        53
        2648505
        0.0287%
        AAGTTGTTAAGTAGCGGTTCTTAAACTTTTAGGTGGTTGAGTATAGGAGT
        31
        1390210
        0.0151%
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        23
        1117535
        0.0121%
        GCCCCACCCAAAAATCTTTTACTTATTAATTCAGCTTAGCTTTTCAAAGT
        16
        844146
        0.0092%
        CTGCGAACAAACAGAATCCTACCTAACCATATCCTTAGCAATATTAAGGC
        9
        408812
        0.0044%
        GTCCTTTCGTACATATTAAGATAATATTATTTAAAGCAGATAGAAACCAA
        8
        393388
        0.0043%
        CTGCGGACAAACAGAATCCTACCTAACCATATCCTTAGCAATATTAAGGC
        8
        337274
        0.0037%
        TGTTAAGTAGCGGTTCTTAAACTTTTAGGTGGTTGAGTATAGGAGTATTA
        8
        304234
        0.0033%
        GGCACTATAAACCCTATTTCTCTTTCTAAAAATTGAAATATTAAAGAAAC
        6
        300062
        0.0033%
        ATTCAACTTTATCTAAAGGAACTCGGCAAATAGTAAGCCTCGCCTGTTTA
        6
        285344
        0.0031%
        GCCCGATTTTGCGTATCACATCCTTAAAGAAATTAGTTCGAGAATTTAGT
        5
        222982
        0.0024%
        GTGGCACTATAAACCCTATTTCTCTTTCTAAAAATTGAAATATTAAAGAA
        4
        214021
        0.0023%
        GCTGCACTTAAAAGCATTTTTTGAACAACCAGCTATCATAAAGCCCGATT
        4
        179530
        0.0019%
        GGAGTATTAGAAAGCCCATAATCTAGCTATATTAAGTCTGACTAGACGCA
        4
        152075
        0.0016%
        Expand table

        Adapter Content
        240

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1